Re: [Rdkit-discuss] SDF tags and "->"

Nicholas Firth Wed, 29 Apr 2015 04:18:08 -0700

I use SD files with new lines in the properties quite frequently (inherited 
from Pipeline Pilot's merge function) and I've never had a problem reading 
them. I've attached an SD file that works fine for me.


In [2]: suppl = Chem.SDMolSupplier('/Volumes/nfirth/tempf.sdf')

In [3]: m = suppl[0]

In [4]: t = m.GetProp('genNum')

In [5]: print t
1
2
3
4

In [6]: print t.split('\n')
['1', '2', '3', '4']


So I guess the problem is in the writer?

Best,
Nick

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tempf.sdf
Description: tempf.sdf

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On 29 Apr 2015, at 11:27, Tuomo Kalliokoski <tkall...@live.com> wrote:

Hello Riccardo,

That sounds very reasonable solution to the issue.

[I replied to rdkit-discuss to bring this thread on the list back again]

Best regards,
Tuomo

From: riccardo.viane...@gmail.com
Date: Wed, 29 Apr 2015 12:08:48 +0200
Subject: Re: [Rdkit-discuss] SDF tags and "->"
To: tkall...@live.com

Hi Tuomo,

yes, I agree the behavior seems a bit inconsistent. I suppose that if the correctness of the parser is confirmed, then a change could be suggested for the writer, consisting in raising an error if blank lines are present inside the data item.

[but once again, I didn't notice the defailt reply-to settings of rdkit-discuss and accidentally brought the thread off-list, sorry.]

Regards,

Riccardo

On Wed, Apr 29, 2015 at 11:46 AM, Tuomo Kalliokoski <tkall...@live.com> wrote:

Hello Riccardo,

Thanks for the swift reply! Indeed, it is the extra line-feed, not the "->". It was just around the same line where I had the issue, so it got me confused.
I suppose the current functionality of RDKit, irrespective to the SDF file format specifications, is a bit odd: SDWriter produces file that SDMolSupplier can't handle.

Best regards,
Tuomo

From: riccardo.viane...@gmail.com
Date: Wed, 29 Apr 2015 11:33:14 +0200
Subject: Re: [Rdkit-discuss] SDF tags and "->"
To: tkall...@live.com

Hi Tuomo,

On Wed, Apr 29, 2015 at 10:47 AM, Tuomo Kalliokoski <tkall...@live.com> wrote:
I have got a bunch of SDF-files with molecules and some long descriptions in SDF-tags on them that include stuff like "->" inside.
These files have been produced by ChemAxon's software and are handled fine by their software.
Such files can be written out also from RDKit 2014_09_02, but they fail when you try to read them in.

I suspect the parse error could be independent from the "->", but due to the blank line ("\n\n") that appears inside the "TESTFIELD" data:

mol.SetProp("TESTFIELD","This should not work -> Let's see\n\nI guess this is not visible\n")

and that is interpreted as the data item terminator. Iirc this interpretation is compliant with the specifications for the SDF file format, but I could be mistaken.

Best regards,
Riccardo

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